Connectors like that generally are a pain (lots of hard-to-access pins, plastic might melt, leading to all kinds of issues). If you get a real, metal stencil, you should get individual apertures. I think the perpendicular bead thing is most relevant when you are manually dispensing solder paste, in which case you should definitely not mess around trying to get a dot on each pad. For a cheap stencil where you are at the limit of the process, I think it's still preferable to go with individual apertures. After you do your print, if you get nice deposits on each pad, great; if not, you can still manually add the bead after that.